The above attached article provides many of the answers to the question and I was prepared to be annoyed with the comments of those who clearly didn’t read the article. In retrospect, I can only think the OP included the article to be illustrative to those who are unfamiliar with the concept of male rape and then wanted a discussion on the specific taboo inherent in male rape (and the associated impact on victims speaking out).
Those who have worked with female rape survivors have long said, “Rape is not a sexual crime, it is a crime of power,” wherein one physically demonstrates that one has greater power over another. Nowhere is the truth of this more clear than with men raping other men.
Because of cultural mores and various taboos about homosexuality (and confusion around rape as a sexual crime), the impact of rape carries an additional psychological element . While a man could be beaten to within an inch of his life, a single rape carries more psychological baggage. In the article, telling men to “assume the Muslim position [of prayer]” adds another psychological element.
The rape of men is not always a war crime, although in war time (like prison settings) those who prey on others seem to take advantage of the situations in which they find themselves. Men are raped in peacetime and, similarly, rarely report it for many of the same taboo reasons.
The article struck me most for the physical damage created. I understand why the men don’t seek help and can’t afford to eat a soft diet for the balance of their lives, but I would hope there could be improvements to the medical care provided for those brave enough to share what happened to them. The stigma would likely not go away, but the constant physical reminder of the incident(s) could certainly be reduced.